Team:Johns Hopkins-BAG/B-A-G course

B-A-G Course

The Build-a-Genome course offers a cool environment in which undergraduate students can participate in cutting-edge interdisciplinary research. In pursuing the synthesis of Saccharomyces cerevisiae Sc2.0 chromosomes, students gain hands-on experience in synthetic biology research. The de novo synthesis of genetic information offers the promise of a deeper understanding of chromosome structure, gene function, and gene order. The ultimate goal of this class is the development of students into skilled, independent researchers with well-developed troubleshooting skills and experience and familiarity with molecular biology and computational approaches to genomics problems.

The Build-a-Genome course consists of lectures, “Molecular Biology Boot Camp”, and eventually, independent research. The lectures offered in the course reflect the many-faceted underpinnings of synthetic biology, ranging in topics from fundamentals of genetics (such as nucleic acid structure and function, chromosome structure, and genome organization) to bioinformatics, to central concepts of synthetic biology (such as recombinant DNA technology, gene synthesis, synthetic circuitry and of course iGEM!). After introductory lectures are complete, students go through eight sessions of molecular biology “boot camp” that serve as a period to review lecture topics, master lab techniques, and learn the methods used in this project. Graduation from the boot camp requires students to submit assignments that verify proficiency in each step of the gene synthesis protocol – such as PCR, agarose gel electrophoresis, molecular cloning, sequence analysis, etc.

An example of a student's colony screening PCR to check for correct inserts after transformation

A screen shot of Build-a-Genome Moodle(Modular Object-Oriented Dynamic Learning Environment) course management software

Once graduated from boot camp, each student is assigned 12-16 building blocks (~10,000 bp) to synthesize. While they are encouraged to work independently and have open 24/7 access to the laboratory, most choose some form of cooperative work and learning, either with their lab partners (assigned during boot camp) or in small groups. Regular “lab meetings” are held in which short student presentations engender group troubleshooting discussions that help students become fluent with scientific language and ensure that they understand concepts well enough to explain their reasoning when altering protocols. Student success is objectively evaluated according to their ability to produce building block DNA (8-10 out of 12-16 assigned) and to complete the entire gene synthesis protocol by generating clones of perfect sequence (at least 3). In the course of one academic year (2 semesters, 1 summer, 1 intersession), the first pass of the entire ~280 kb synthetic chromosome III sequence was achieved.

Overall, the Build-a-Genome course has proven to be successful. Student evaluations of the course were greatly positive, and many students became mentors or continued with side projects after completing the course. Build-a-Genome will undoubtedly remain a challenging and popular course at Johns Hopkins.